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+<title>MayaChemTools:Code:MolecularDescriptors::MolecularVolumeDescriptors.pm</title>
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+<a name="package-MolecularDescriptors::MolecularVolumeDescriptors-"></a>   1 <span class="k">package </span><span class="i">MolecularDescriptors::MolecularVolumeDescriptors</span><span class="sc">;</span>
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: MolecularVolumeDescriptors.pm,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span>
+   5 <span class="c"># $Revision: 1.16 $</span>
+   6 <span class="c">#</span>
+   7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+   8 <span class="c">#</span>
+   9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+  10 <span class="c">#</span>
+  11 <span class="c"># This file is part of MayaChemTools.</span>
+  12 <span class="c">#</span>
+  13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+  14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+  15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+  16 <span class="c"># later version.</span>
+  17 <span class="c">#</span>
+  18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+  19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+  20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+  21 <span class="c"># details.</span>
+  22 <span class="c">#</span>
+  23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+  24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+  25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+  26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+  27 <span class="c">#</span>
+  28 
+  29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+  30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
+  31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
+  32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  34 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  35 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span>
+  36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
+  37 <span class="k">use</span> <span class="w">AtomTypes::AtomTypes</span><span class="sc">;</span>
+  38 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span>
+  39 
+  40 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span>
+  41 
+  42 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span>
+  43 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
+  44 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames GetVDWAtomRadiiAndVolumesData)</span><span class="sc">;</span>
+  45 
+  46 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span>  <span class="cm">=&gt;</span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span>
+  47 
+  48 <span class="c"># Setup class variables...</span>
+  49 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="i">%VDWAtomRadiiAndVolumesDataMap</span><span class="s">)</span><span class="sc">;</span>
+  50 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  51 
+  52 <span class="c"># Overload Perl functions...</span>
+  53 <span class="k">use</span> <span class="w">overload</span> <span class="q">&#39;&quot;&quot;&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;StringifyMolecularVolumeDescriptors&#39;</span><span class="sc">;</span>
+  54 
+  55 <span class="c"># Class constructor...</span>
+<a name="new-"></a>  56 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
+  57   <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  58 
+  59   <span class="c"># Initialize object...</span>
+  60   <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  61   <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span>
+  62   <span class="i">$This</span><span class="i">-&gt;_InitializeMolecularVolumeDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  63 
+  64   <span class="i">$This</span><span class="i">-&gt;_InitializeMolecularVolumeDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
+  65 
+  66   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+  67 <span class="s">}</span>
+  68 
+  69 <span class="c"># Initialize class ...</span>
+<a name="_InitializeClass-"></a>  70 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
+  71   <span class="c">#Class name...</span>
+  72   <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
+  73 
+  74   <span class="c"># Descriptor names...</span>
+  75   <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">&#39;MolecularVolume&#39;</span><span class="s">)</span><span class="sc">;</span>
+  76 
+  77   <span class="c"># Initialize the data hash. It&#39;ll be loaded on demand later...</span>
+  78   <span class="i">%VDWAtomRadiiAndVolumesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  79 
+  80 <span class="s">}</span>
+  81 
+  82 <span class="c"># Get descriptor names as an array.</span>
+  83 <span class="c">#</span>
+  84 <span class="c"># This functionality can be either invoked as a class function or an</span>
+  85 <span class="c"># object method.</span>
+  86 <span class="c">#</span>
+<a name="GetDescriptorNames-"></a>  87 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span>
+  88   <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
+  89 <span class="s">}</span>
+  90 
+  91 <span class="c"># Initialize object data...</span>
+  92 <span class="c">#</span>
+<a name="_InitializeMolecularVolumeDescriptors-"></a>  93 <span class="k">sub </span><span class="m">_InitializeMolecularVolumeDescriptors</span> <span class="s">{</span>
+  94   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  95 
+  96   <span class="c"># Type of MolecularDescriptor...</span>
+  97   <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;MolecularVolume&#39;</span><span class="sc">;</span>
+  98 
+  99   <span class="c"># Intialize descriptor names and values...</span>
+ 100   <span class="i">$This</span><span class="i">-&gt;_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
+ 101 
+ 102   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 103 <span class="s">}</span>
+ 104 
+ 105 <span class="c"># Initialize object properties...</span>
+ 106 <span class="c">#</span>
+<a name="_InitializeMolecularVolumeDescriptorsProperties-"></a> 107 <span class="k">sub </span><span class="m">_InitializeMolecularVolumeDescriptorsProperties</span> <span class="s">{</span>
+ 108   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 109 
+ 110   <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span>
+ 111   <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span>  <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
+ 112     <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
+ 113     <span class="i">$This</span><span class="i">-&gt;$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
+ 114   <span class="s">}</span>
+ 115 
+ 116   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 117 <span class="s">}</span>
+ 118 
+ 119 <span class="c"># Get VDW atom data loaded from VDW atom radii and and volumes data file as</span>
+ 120 <span class="c"># a reference to hash with the following hash data format:</span>
+ 121 <span class="c">#</span>
+ 122 <span class="c"># @{$VDWAtomRadiiAndVolumesDataMap{AtomTypes}} - Array of all possible atom type symbols for all atoms</span>
+ 123 <span class="c"># @{$VDWAtomRadiiAndVolumesDataMap-&gt;{ColLabels}} - Array of column labels</span>
+ 124 <span class="c"># %{$VDWAtomRadiiAndVolumesDataMap-&gt;{DataCol&lt;Num&gt;}} - Hash keys pair: &lt;DataCol&lt;Num&gt;, AtomType&gt;</span>
+ 125 <span class="c">#</span>
+ 126 <span class="c"># This functionality can be either invoked as a class function or an</span>
+ 127 <span class="c"># object method.</span>
+ 128 <span class="c">#</span>
+<a name="GetVDWAtomRadiiAndVolumesData-"></a> 129 <span class="k">sub </span><span class="m">GetVDWAtomRadiiAndVolumesData</span> <span class="s">{</span>
+ 130 
+ 131   <span class="c"># Make sure data is loaded...</span>
+ 132   <span class="i">_CheckAndLoadVDWAtomRadiiAndVolumesData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 133 
+ 134   <span class="k">return</span> \<span class="i">%VDWAtomRadiiAndVolumesDataMap</span><span class="sc">;</span>
+ 135 <span class="s">}</span>
+ 136 
+ 137 <span class="c"># Calculate van der Waals molecular volume [ Ref 93 ] of a molecule using</span>
+ 138 <span class="c"># atomic and bonds contributions...</span>
+ 139 <span class="c">#</span>
+ 140 <span class="c"># van der Waals molecular volume (A**3/molecule) is defined as:</span>
+ 141 <span class="c">#</span>
+ 142 <span class="c"># vdwMolecularVolume = SumOfAtomicVDWVolumeContributions - 5.92 * NumOfBonds</span>
+ 143 <span class="c">#                      - 14.7 * NumOfAromaticRings - 3.8 * NumOfNonAromaticRings</span>
+ 144 <span class="c">#</span>
+ 145 <span class="c"># Methodology:</span>
+ 146 <span class="c">#   . Add up van der Waals atom volumne of all atoms</span>
+ 147 <span class="c">#   . Calculate molecular volume by correcting sum of atom volumes for num of</span>
+ 148 <span class="c">#     bonds and rings</span>
+ 149 <span class="c">#</span>
+ 150 <span class="c"># Caveats:</span>
+ 151 <span class="c">#   . All hydrogens must be added to molecule before calling GenerateDescriptors.</span>
+ 152 <span class="c">#</span>
+<a name="GenerateDescriptors-"></a> 153 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
+ 154   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 155 
+ 156   <span class="c"># Initialize descriptor values...</span>
+ 157   <span class="i">$This</span><span class="i">-&gt;_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 158 
+ 159   <span class="c"># Check availability of molecule...</span>
+ 160   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
+ 161     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Molecule data is not available: Molecule object hasn&#39;t been set...&quot;</span><span class="sc">;</span>
+ 162     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 163   <span class="s">}</span>
+ 164 
+ 165   <span class="c"># Calculate descriptor values...</span>
+ 166   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 167     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Couldn&#39;t calculate MolecularVolume values: van der Waals atom volume data is not available for all atoms...&quot;</span><span class="sc">;</span>
+ 168     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 169   <span class="s">}</span>
+ 170 
+ 171   <span class="c"># Set final descriptor values...</span>
+ 172   <span class="i">$This</span><span class="i">-&gt;_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 173 
+ 174   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 175 <span class="s">}</span>
+ 176 
+ 177 <span class="c"># Calculate MolecularVolume value...</span>
+ 178 <span class="c">#</span>
+<a name="_CalculateDescriptorValues-"></a> 179 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span>
+ 180   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 181   <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$SumOfVDWAtomVolumes</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$MolecularVolume</span><span class="cm">,</span> <span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticRings</span><span class="cm">,</span> <span class="i">$NumOfNonAromaticRings</span><span class="cm">,</span> <span class="i">$VDWAtomRadiiAndVolumesDataMapRef</span><span class="s">)</span><span class="sc">;</span>
+ 182 
+ 183   <span class="i">$MolecularVolume</span> = <span class="n">0</span><span class="sc">;</span>
+ 184 
+ 185   <span class="i">$VDWAtomRadiiAndVolumesDataMapRef</span> = <span class="i">$This</span><span class="i">-&gt;GetVDWAtomRadiiAndVolumesData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 186   <span class="i">$Molecule</span> = <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="sc">;</span>
+ 187 
+ 188   <span class="c"># Calculate atom volumes contribution to molecular volume...</span>
+ 189   <span class="c">#</span>
+ 190   <span class="i">$SumOfVDWAtomVolumes</span> = <span class="n">0</span><span class="sc">;</span>
+ 191 
+ 192   <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 193     <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 194     <span class="i">$AtomSymbol</span> = <span class="i">$Atom</span><span class="i">-&gt;GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 195 
+ 196     <span class="c"># Make sure van der Waals atom volume is available...</span>
+ 197     <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$VDWAtomRadiiAndVolumesDataMap</span>{<span class="w">DataCol3</span>}{<span class="i">$AtomSymbol</span>}<span class="s">)</span> <span class="s">{</span>
+ 198       <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 199     <span class="s">}</span>
+ 200     <span class="i">$SumOfVDWAtomVolumes</span> += <span class="i">$VDWAtomRadiiAndVolumesDataMapRef</span>-&gt;{<span class="w">DataCol3</span>}{<span class="i">$AtomSymbol</span>}<span class="sc">;</span>
+ 201   <span class="s">}</span>
+ 202 
+ 203   <span class="i">$NumOfBonds</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetNumOfBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 204   <span class="i">$NumOfAromaticRings</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetNumOfAromaticRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 205   <span class="i">$NumOfNonAromaticRings</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetNumOfRings</span><span class="s">(</span><span class="s">)</span> - <span class="i">$NumOfAromaticRings</span><span class="sc">;</span>
+ 206 
+ 207   <span class="c"># Apply correction for bonds and rings...</span>
+ 208   <span class="i">$MolecularVolume</span> = <span class="i">$SumOfVDWAtomVolumes</span> - <span class="n">5.92</span> * <span class="i">$NumOfBonds</span> - <span class="n">14.7</span> * <span class="i">$NumOfAromaticRings</span> - <span class="n">3.8</span> * <span class="i">$NumOfNonAromaticRings</span><span class="sc">;</span>
+ 209 
+ 210   <span class="c"># Track the calculated values...</span>
+ 211   <span class="i">$This</span>-&gt;{<span class="w">MolecularVolume</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$MolecularVolume</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span>
+ 212 
+ 213   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 214 <span class="s">}</span>
+ 215 
+ 216 <span class="c"># Setup final descriptor values...</span>
+ 217 <span class="c">#</span>
+<a name="_SetFinalDescriptorValues-"></a> 218 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span>
+ 219   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 220 
+ 221   <span class="i">$This</span>-&gt;{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
+ 222 
+ 223   <span class="i">$This</span><span class="i">-&gt;SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MolecularVolume</span>}<span class="s">)</span><span class="sc">;</span>
+ 224 
+ 225   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 226 <span class="s">}</span>
+ 227 
+ 228 <span class="c"># Return a string containg data for MolecularVolumeDescriptors object...</span>
+ 229 <span class="c">#</span>
+<a name="StringifyMolecularVolumeDescriptors-"></a> 230 <span class="k">sub </span><span class="m">StringifyMolecularVolumeDescriptors</span> <span class="s">{</span>
+ 231   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 232   <span class="k">my</span><span class="s">(</span><span class="i">$MolecularVolumeDescriptorsString</span><span class="s">)</span><span class="sc">;</span>
+ 233 
+ 234   <span class="i">$MolecularVolumeDescriptorsString</span> = <span class="q">&quot;MolecularDescriptorType: $This-&gt;{Type}; &quot;</span> . <span class="i">$This</span><span class="i">-&gt;_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 235 
+ 236   <span class="k">return</span> <span class="i">$MolecularVolumeDescriptorsString</span><span class="sc">;</span>
+ 237 <span class="s">}</span>
+ 238 
+ 239 <span class="c"># Is it a MolecularVolumeDescriptors object?</span>
+<a name="_IsMolecularVolumeDescriptors-"></a> 240 <span class="k">sub </span><span class="m">_IsMolecularVolumeDescriptors</span> <span class="s">{</span>
+ 241   <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 242 
+ 243   <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> &amp;&amp; <span class="i">$Object</span><span class="i">-&gt;isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 244 <span class="s">}</span>
+ 245 
+ 246 <span class="c"># Check and load van der Waals atom radii and volumes data...</span>
+ 247 <span class="c">#</span>
+<a name="_CheckAndLoadVDWAtomRadiiAndVolumesData-"></a> 248 <span class="k">sub </span><span class="m">_CheckAndLoadVDWAtomRadiiAndVolumesData</span> <span class="s">{</span>
+ 249 
+ 250   <span class="c"># Is it already loaded?</span>
+ 251   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$VDWAtomRadiiAndVolumesDataMap</span>{<span class="w">AtomTypes</span>}<span class="s">)</span> <span class="s">{</span>
+ 252     <span class="k">return</span><span class="sc">;</span>
+ 253   <span class="s">}</span>
+ 254 
+ 255   <span class="i">_LoadVDWAtomRadiiAndVolumesData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 256 <span class="s">}</span>
+ 257 
+ 258 <span class="c"># Initialize van der Waals atom radii and volumes data from the file...</span>
+ 259 <span class="c">#</span>
+ 260 <span class="c"># Format:</span>
+ 261 <span class="c">#</span>
+ 262 <span class="c"># &quot;AtomTypeSymbol&quot;,&quot;VDWAtomRadius(A)&quot;,&quot;VDWAtomVolume(A**3)/molecule&quot;</span>
+ 263 <span class="c"># &quot;H&quot;,&quot;1.20&quot;,&quot;7.24&quot;</span>
+ 264 <span class="c"># &quot;He&quot;,&quot;1.40&quot;,&quot;11.49&quot;</span>
+ 265 <span class="c">#</span>
+<a name="_LoadVDWAtomRadiiAndVolumesData-"></a> 266 <span class="k">sub  </span><span class="m">_LoadVDWAtomRadiiAndVolumesData</span> <span class="s">{</span>
+ 267   <span class="k">my</span><span class="s">(</span><span class="i">$VDWAtomDataFile</span><span class="cm">,</span> <span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span>
+ 268 
+ 269   <span class="i">$MayaChemToolsLibDir</span> = <span class="i">FileUtil::GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 270 
+ 271   <span class="i">$VDWAtomDataFile</span> =  <span class="q">&quot;$MayaChemToolsLibDir&quot;</span> . <span class="q">&quot;/data/VDWAtomRadiiAndVolumes.csv&quot;</span><span class="sc">;</span>
+ 272   <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">&quot;$VDWAtomDataFile&quot;</span><span class="s">)</span> <span class="s">{</span>
+ 273     <span class="w">croak</span> <span class="q">&quot;Error: MayaChemTools package file, $VDWAtomDataFile, is missing: Possible installation problems...&quot;</span><span class="sc">;</span>
+ 274   <span class="s">}</span>
+ 275 
+ 276   <span class="i">%VDWAtomRadiiAndVolumesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 277   <span class="i">AtomTypes::AtomTypes::LoadAtomTypesData</span><span class="s">(</span><span class="i">$VDWAtomDataFile</span><span class="cm">,</span> \<span class="i">%VDWAtomRadiiAndVolumesDataMap</span><span class="s">)</span><span class="sc">;</span>
+ 278 <span class="s">}</span><span class="sc">;</span>
+ 279 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>